ESD4_ARATH
ID ESD4_ARATH Reviewed; 489 AA.
AC Q94F30; B9DFG4; O23439; Q70G10; Q7DLT0;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=Ubiquitin-like-specific protease ESD4;
DE EC=3.4.22.68;
DE AltName: Full=Protein EARLY IN SHORT DAYS 4;
DE Short=AtESD4;
GN Name=ESD4; OrderedLocusNames=At4g15880; ORFNames=dl3980w, FCAALL.406;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, REGULATION, INDUCTION, MUTAGENESIS OF
RP CYS-448, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=14507998; DOI=10.1105/tpc.015487;
RA Murtas G., Reeves P.H., Fu Y.F., Bancroft I., Dean C., Coupland G.;
RT "A nuclear protease required for flowering-time regulation in Arabidopsis
RT reduces the abundance of SMALL UBIQUITIN-RELATED MODIFIER conjugates.";
RL Plant Cell 15:2308-2319(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-422.
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] OF 46-441.
RC TISSUE=Dry seed;
RX PubMed=9358062; DOI=10.1016/s0378-1119(97)00374-0;
RA Aubourg S., Takvorian A., Cheron A., Kreis M., Lecharny A.;
RT "Structure, organization and putative function of the genes identified
RT within a 23.9 kb fragment from Arabidopsis thaliana chromosome IV sequenced
RT in the framework of the ESSA programme.";
RL Gene 199:241-253(1997).
RN [8]
RP FUNCTION.
RX PubMed=16740136; DOI=10.1042/bj20060426;
RA Chosed R., Mukherjee S., Lois L.M., Orth K.;
RT "Evolution of a signalling system that incorporates both redundancy and
RT diversity: Arabidopsis SUMOylation.";
RL Biochem. J. 398:521-529(2006).
RN [9]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16920872; DOI=10.1104/pp.106.085415;
RA Colby T., Matthai A., Boeckelmann A., Stuible H.P.;
RT "SUMO-conjugating and SUMO-deconjugating enzymes from Arabidopsis.";
RL Plant Physiol. 142:318-332(2006).
RN [10]
RP INTERACTION WITH NUA, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=17513499; DOI=10.1105/tpc.106.049239;
RA Xu X.M., Rose A., Muthuswamy S., Jeong S.Y., Venkatakrishnan S., Zhao Q.,
RA Meier I.;
RT "NUCLEAR PORE ANCHOR, the Arabidopsis homolog of Tpr/Mlp1/Mlp2/megator, is
RT involved in mRNA export and SUMO homeostasis and affects diverse aspects of
RT plant development.";
RL Plant Cell 19:1537-1548(2007).
RN [11]
RP INTERACTION WITH NUA.
RX PubMed=19704557; DOI=10.4161/psb.2.6.4836;
RA Xu X.M., Rose A., Meier I.;
RT "NUA Activities at the Plant Nuclear Pore.";
RL Plant Signal. Behav. 2:553-555(2007).
RN [12]
RP INTERACTION WITH KIN10.
RX PubMed=20855607; DOI=10.1073/pnas.1005452107;
RA Elrouby N., Coupland G.;
RT "Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates
RT identify Arabidopsis proteins implicated in diverse biological processes.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:17415-17420(2010).
CC -!- FUNCTION: Protease that catalyzes two essential functions in the SUMO
CC pathway: processing of full-length SUMOs to their mature forms and
CC deconjugation of SUMO from targeted proteins. Cleaves precursors of
CC SUM1 and SUM2, but not of SUM3 or SUM5. Able to release SUM1 and SUM2
CC from conjugates, but unable to cleave SUM3. Acts predominantly as an
CC isopeptidase, cleaving SUMO-conjugated proteins better than SUMO
CC peptides. Plays an important role in the control of flowering time.
CC {ECO:0000269|PubMed:14507998, ECO:0000269|PubMed:16740136}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of the alpha-linked peptide bond in the sequence
CC Gly-Gly-|-Ala-Thr-Tyr at the C-terminal end of the small ubiquitin-
CC like modifier (SUMO) propeptide, Smt3, leading to the mature form of
CC the protein. A second reaction involves the cleavage of an epsilon-
CC linked peptide bond between the C-terminal glycine of the mature SUMO
CC and the lysine epsilon-amino group of the target protein.;
CC EC=3.4.22.68;
CC -!- ACTIVITY REGULATION: Inhibited by thiol reagent and N-ethylmaleimide,
CC but not by ubiquitin aldehyde, pepstatin A or benzamidine HCl.
CC -!- SUBUNIT: Interacts with NUA (via N-terminus). Interacts with KIN10
CC (PubMed:20855607). {ECO:0000269|PubMed:17513499,
CC ECO:0000269|PubMed:19704557, ECO:0000269|PubMed:20855607}.
CC -!- SUBCELLULAR LOCATION: Nucleus membrane {ECO:0000269|PubMed:14507998,
CC ECO:0000269|PubMed:17513499}; Peripheral membrane protein
CC {ECO:0000269|PubMed:14507998, ECO:0000269|PubMed:17513499}. Note=The
CC nuclear envelope localization is independent of the presence of the
CC nuclear pore anchor NUA.
CC -!- TISSUE SPECIFICITY: Expressed in seedlings, leaves, shoots, flowers and
CC roots. {ECO:0000269|PubMed:14507998}.
CC -!- INDUCTION: No circadian regulation. {ECO:0000269|PubMed:14507998}.
CC -!- DOMAIN: The N-terminal regulatory domain is required for peptidase
CC activity in vitro.
CC -!- DISRUPTION PHENOTYPE: Early flowering under both long and short days
CC and pleiotropic alterations in shoot development.
CC {ECO:0000269|PubMed:14507998, ECO:0000269|PubMed:17513499}.
CC -!- SIMILARITY: Belongs to the peptidase C48 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB45994.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78630.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AJ582719; CAE46910.1; -; mRNA.
DR EMBL; Z97339; CAB45994.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161542; CAB78630.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE83661.1; -; Genomic_DNA.
DR EMBL; AF386934; AAK62379.1; -; mRNA.
DR EMBL; AY081548; AAM10110.1; -; mRNA.
DR EMBL; AK316760; BAH19481.1; -; mRNA.
DR EMBL; Y11155; CAA72042.1; -; mRNA.
DR EMBL; Y11187; CAA72071.1; -; Genomic_DNA.
DR PIR; E71424; E71424.
DR PIR; H85175; H85175.
DR RefSeq; NP_567478.1; NM_117680.4.
DR AlphaFoldDB; Q94F30; -.
DR SMR; Q94F30; -.
DR BioGRID; 12563; 1.
DR IntAct; Q94F30; 1.
DR STRING; 3702.AT4G15880.1; -.
DR MEROPS; C48.022; -.
DR iPTMnet; Q94F30; -.
DR PaxDb; Q94F30; -.
DR PRIDE; Q94F30; -.
DR ProteomicsDB; 220577; -.
DR EnsemblPlants; AT4G15880.1; AT4G15880.1; AT4G15880.
DR GeneID; 827269; -.
DR Gramene; AT4G15880.1; AT4G15880.1; AT4G15880.
DR KEGG; ath:AT4G15880; -.
DR Araport; AT4G15880; -.
DR TAIR; locus:2130864; AT4G15880.
DR eggNOG; KOG0778; Eukaryota.
DR HOGENOM; CLU_024324_6_2_1; -.
DR InParanoid; Q94F30; -.
DR OMA; HREIHWC; -.
DR OrthoDB; 1480705at2759; -.
DR PhylomeDB; Q94F30; -.
DR BRENDA; 3.4.22.68; 399.
DR PRO; PR:Q94F30; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q94F30; baseline and differential.
DR Genevisible; Q94F30; AT.
DR GO; GO:0031965; C:nuclear membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0016929; F:deSUMOylase activity; IBA:GO_Central.
DR GO; GO:0019900; F:kinase binding; IPI:UniProtKB.
DR GO; GO:0070139; F:SUMO-specific endopeptidase activity; IDA:UniProtKB.
DR GO; GO:0009911; P:positive regulation of flower development; IMP:TAIR.
DR GO; GO:0016926; P:protein desumoylation; IDA:UniProtKB.
DR GO; GO:0009909; P:regulation of flower development; IMP:TAIR.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR003653; Peptidase_C48_C.
DR Pfam; PF02902; Peptidase_C48; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS50600; ULP_PROTEASE; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Hydrolase; Membrane; Nucleus; Protease; Reference proteome;
KW Thiol protease; Ubl conjugation pathway.
FT CHAIN 1..489
FT /note="Ubiquitin-like-specific protease ESD4"
FT /id="PRO_0000395972"
FT REGION 43..66
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 200..223
FT /evidence="ECO:0000255"
FT COMPBIAS 47..61
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 380
FT /evidence="ECO:0000250"
FT ACT_SITE 397
FT /evidence="ECO:0000250"
FT ACT_SITE 448
FT /evidence="ECO:0000250"
FT MUTAGEN 448
FT /note="C->S: Loss of protease activity."
FT /evidence="ECO:0000269|PubMed:14507998"
FT CONFLICT 325
FT /note="K -> P (in Ref. 1; CAE46910)"
FT /evidence="ECO:0000305"
FT CONFLICT 331
FT /note="H -> L (in Ref. 1; CAE46910)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 489 AA; 56426 MW; 2A1EA3CE19B19408 CRC64;
MGAVAINRKR SDESFNFINQ QSTNPLRNSP YFQASKKRRF SFAMSEDSGK PASSNPTISR
ISRYPDAKAP LRREIHAPSR GILRYGKAKS NDYCEKDANF FVRKYDDAKR SALEALRFVN
KGKDFVDLGD EVEKEEVVSD DSSVQAIEVI DCDDDEEKKN LQPSFSSGVT DVKKGENFRV
EDTSMMLDSL SLDRDVDNDA SSLEAYRKLM QSAEKRNSKL EALGFEIVLN EKKLSLLRQS
RPKTVEKRVE VPREPFIPLT EDEEAEVYRA FSGRNRRKVL ATHENSNIDI TGEVLQCLTP
SAWLNDEVIN VYLELLKERE TREPKKYLKC HYFNTFFYKK LVSDSGYNFK AVRRWTTQRK
LGYALIDCDM IFVPIHRGVH WTLAVINNRE SKLLYLDSLN GVDPMILNAL AKYMGDEANE
KSGKKIDANS WDMEFVEDLP QQKNGYDCGM FMLKYIDFFS RGLGLCFSQE HMPYFRLRTA
KEILRLRAD
